4qm6 - Revision history

OCA at 12:47, 1 March 2024

OCA — Fri, 01 Mar 2024 12:47:10 GMT

←Older revision		Revision as of 12:47, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4qm6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Acetivibrio_thermocellus_ATCC_27405 Acetivibrio thermocellus ATCC 27405]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QM6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QM6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4qm6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Acetivibrio_thermocellus_ATCC_27405 Acetivibrio thermocellus ATCC 27405]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QM6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QM6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.5Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4qm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qm6 OCA], [https://pdbe.org/4qm6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qm6 RCSB], [https://www.ebi.ac.uk/pdbsum/4qm6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qm6 ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4qm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qm6 OCA], [https://pdbe.org/4qm6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qm6 RCSB], [https://www.ebi.ac.uk/pdbsum/4qm6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qm6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/A3DJ38_ACET2 A3DJ38_ACET2]		[https://www.uniprot.org/uniprot/A3DJ38_ACET2 A3DJ38_ACET2]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Clostridium thermocellum polynucleotide kinase (CthPnk), the 5' end-healing module of a bacterial RNA repair system, catalyzes reversible phosphoryl transfer from an NTP donor to a 5'-OH polynucleotide acceptor, either DNA or RNA. Here we report the 1.5 A crystal structure of CthPnk-D38N in a Michaelis complex with GTPMg2+ and a 5'-OH RNA oligonucleotide. The RNA-binding mode of CthPnk is different from that of the metazoan RNA kinase Clp1. CthPnk makes hydrogen bonds to the ribose 2'-hydroxyls of the 5' terminal nucleoside, via Gln51, and the penultimate nucleoside, via Gln83. The 5' terminal nucleobase is sandwiched by Gln51 and Val129. Mutating Gln51 or Val129 to alanine reduced kinase specific activity by 3-fold. Ser37 and Thr80 donate functionally redundant hydrogen bonds to the terminal phosphodiester; a S37A-T80A double mutation reduced kinase activity by 50-fold. Crystallization of catalytically active CthPnk with GTPMg2+ and a 5'-OH DNA yielded a mixed substrate/product complex with GTP*Mg2+ and 5'-PO4 DNA, wherein the product 5'-phosphate group is displaced by the NTP gamma phosphate and the local architecture of the acceptor site is perturbed.
-
-	Structures of bacterial polynucleotide kinase in a Michaelis complex with NTPMg2+ and 5'-OH RNA and a mixed substrate-product complex with NTPMg2+ and a 5'-phosphorylated oligonucleotide.,Das U, Wang LK, Smith P, Munir A, Shuman S J Bacteriol. 2014 Sep 29. pii: JB.02197-14. PMID:25266383<ref>PMID:25266383</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4qm6" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:35, 15 February 2023

OCA — Wed, 15 Feb 2023 11:35:25 GMT

←Older revision		Revision as of 11:35, 15 February 2023
Line 3:		Line 3:
	<StructureSection load='4qm6' size='340' side='right'caption='[[4qm6]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='4qm6' size='340' side='right'caption='[[4qm6]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4qm6]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Cloth Cloth~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QM6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4QM6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4qm6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Acetivibrio_thermocellus_ATCC_27405 Acetivibrio thermocellus ATCC 27405]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QM6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QM6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mde\|4mde]], [[4mdf\|4mdf]], [[4jsy\|4jsy]], [[4jt2\|4jt2]], [[4jt4\|4jt4]], [[4jst\|4jst]], [[4qm7\|4qm7]]</td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4qm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qm6 OCA], [https://pdbe.org/4qm6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qm6 RCSB], [https://www.ebi.ac.uk/pdbsum/4qm6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qm6 ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Cthe_2768 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=203119 CLOTH])~~</td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4qm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qm6 OCA], [~~http~~://pdbe.org/4qm6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4qm6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4qm6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4qm6 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A3DJ38_ACET2 A3DJ38_ACET2]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Cloth~~]]	+	[[Category: Acetivibrio thermocellus ATCC 27405]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Das, U]]	+	[[Category: Das U]]
-	[[Category: Shuman, S]]	+	[[Category: Shuman S]]
-	[[Category: Smith, P]]	+	[[Category: Smith P]]
-	[[Category: Wang~~, L K]]~~	+	[[Category: Wang LK]]
-	~~[[Category: Hydrolase-rna complex]]~~	+
-	~~[[Category: P-loop phosphotransferase]]~~	+
-	~~[[Category: Polynucleotide kinase]]~~	+
-	~~[[Category: Rna repair]]~~	+
-	~~[[Category: Transferase-rna complex~~]]	+

OCA at 09:01, 24 April 2019

OCA — Wed, 24 Apr 2019 09:01:15 GMT

←Older revision		Revision as of 09:01, 24 April 2019
Line 1:		Line 1:

	==Structure of bacterial polynucleotide kinase bound to GTP and RNA==		==Structure of bacterial polynucleotide kinase bound to GTP and RNA==
-	<StructureSection load='4qm6' size='340' side='right' caption='[[4qm6]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='4qm6' size='340' side='right'caption='[[4qm6]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4qm6]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QM6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QM6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4qm6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Cloth Cloth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QM6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QM6 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mde\|4mde]], [[4mdf\|4mdf]], [[4jsy\|4jsy]], [[4jt2\|4jt2]], [[4jt4\|4jt4]], [[4jst\|4jst]], [[4qm7\|4qm7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mde\|4mde]], [[4mdf\|4mdf]], [[4jsy\|4jsy]], [[4jt2\|4jt2]], [[4jt4\|4jt4]], [[4jst\|4jst]], [[4qm7\|4qm7]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Cthe_2768 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=203119 CLOTH])</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4qm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qm6 OCA], [http://pdbe.org/4qm6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qm6 RCSB], [http://www.ebi.ac.uk/pdbsum/4qm6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qm6 ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4qm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qm6 OCA], [http://pdbe.org/4qm6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qm6 RCSB], [http://www.ebi.ac.uk/pdbsum/4qm6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qm6 ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Cloth]]
		+	[[Category: Large Structures]]
	[[Category: Das, U]]		[[Category: Das, U]]
	[[Category: Shuman, S]]		[[Category: Shuman, S]]

OCA at 17:12, 4 January 2017

OCA — Wed, 04 Jan 2017 17:12:45 GMT

←Older revision		Revision as of 17:12, 4 January 2017
Line 1:		Line 1:
		+
	==Structure of bacterial polynucleotide kinase bound to GTP and RNA==		==Structure of bacterial polynucleotide kinase bound to GTP and RNA==
	<StructureSection load='4qm6' size='340' side='right' caption='[[4qm6]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='4qm6' size='340' side='right' caption='[[4qm6]], [[Resolution\|resolution]] 1.50Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mde\|4mde]], [[4mdf\|4mdf]], [[4jsy\|4jsy]], [[4jt2\|4jt2]], [[4jt4\|4jt4]], [[4jst\|4jst]], [[4qm7\|4qm7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mde\|4mde]], [[4mdf\|4mdf]], [[4jsy\|4jsy]], [[4jt2\|4jt2]], [[4jt4\|4jt4]], [[4jst\|4jst]], [[4qm7\|4qm7]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4qm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qm6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qm6 RCSB], [http://www.ebi.ac.uk/pdbsum/4qm6 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4qm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qm6 OCA], [http://pdbe.org/4qm6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qm6 RCSB], [http://www.ebi.ac.uk/pdbsum/4qm6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qm6 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4qm6" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:18, 20 January 2015

OCA — Tue, 20 Jan 2015 10:18:08 GMT

←Older revision		Revision as of 10:18, 20 January 2015
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Das, U.]]	+	[[Category: Das, U]]
-	[[Category: Shuman, S.]]	+	[[Category: Shuman, S]]
-	[[Category: Smith, P.]]	+	[[Category: Smith, P]]
-	[[Category: Wang, L K.]]	+	[[Category: Wang, L K]]
	[[Category: Hydrolase-rna complex]]		[[Category: Hydrolase-rna complex]]
	[[Category: P-loop phosphotransferase]]		[[Category: P-loop phosphotransferase]]

OCA at 07:37, 8 October 2014

OCA — Wed, 08 Oct 2014 07:37:34 GMT

←Older revision		Revision as of 07:37, 8 October 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Structure of bacterial polynucleotide kinase bound to GTP and RNA==
		+	<StructureSection load='4qm6' size='340' side='right' caption='[[4qm6]], [[Resolution\|resolution]] 1.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4qm6]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QM6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QM6 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mde\|4mde]], [[4mdf\|4mdf]], [[4jsy\|4jsy]], [[4jt2\|4jt2]], [[4jt4\|4jt4]], [[4jst\|4jst]], [[4qm7\|4qm7]]</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4qm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qm6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qm6 RCSB], [http://www.ebi.ac.uk/pdbsum/4qm6 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Clostridium thermocellum polynucleotide kinase (CthPnk), the 5' end-healing module of a bacterial RNA repair system, catalyzes reversible phosphoryl transfer from an NTP donor to a 5'-OH polynucleotide acceptor, either DNA or RNA. Here we report the 1.5 A crystal structure of CthPnk-D38N in a Michaelis complex with GTPMg2+ and a 5'-OH RNA oligonucleotide. The RNA-binding mode of CthPnk is different from that of the metazoan RNA kinase Clp1. CthPnk makes hydrogen bonds to the ribose 2'-hydroxyls of the 5' terminal nucleoside, via Gln51, and the penultimate nucleoside, via Gln83. The 5' terminal nucleobase is sandwiched by Gln51 and Val129. Mutating Gln51 or Val129 to alanine reduced kinase specific activity by 3-fold. Ser37 and Thr80 donate functionally redundant hydrogen bonds to the terminal phosphodiester; a S37A-T80A double mutation reduced kinase activity by 50-fold. Crystallization of catalytically active CthPnk with GTPMg2+ and a 5'-OH DNA yielded a mixed substrate/product complex with GTP*Mg2+ and 5'-PO4 DNA, wherein the product 5'-phosphate group is displaced by the NTP gamma phosphate and the local architecture of the acceptor site is perturbed.

-	~~The entry 4qm6 is ON HOLD until Paper Publication~~	+	Structures of bacterial polynucleotide kinase in a Michaelis complex with NTPMg2+ and 5'-OH RNA and a mixed substrate-product complex with NTPMg2+ and a 5'-phosphorylated oligonucleotide.,Das U, Wang LK, Smith P, Munir A, Shuman S J Bacteriol. 2014 Sep 29. pii: JB.02197-14. PMID:25266383<ref>PMID:25266383</ref>

-	~~Authors~~: Das, U., ~~Wang, L~~.~~K.,~~ Smith, P., ~~Shuman, S~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Structure of bacterial polynucleotide~~ kinase ~~bound to GTP and RNA~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Das, U.]]
		+	[[Category: Shuman, S.]]
		+	[[Category: Smith, P.]]
		+	[[Category: Wang, L K.]]
		+	[[Category: Hydrolase-rna complex]]
		+	[[Category: P-loop phosphotransferase]]
		+	[[Category: Polynucleotide kinase]]
		+	[[Category: Rna repair]]
		+	[[Category: Transferase-rna complex]]

OCA at 09:46, 16 July 2014

OCA — Wed, 16 Jul 2014 09:46:18 GMT

←Older revision		Revision as of 09:46, 16 July 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4qm6 is ON HOLD	+	The entry 4qm6 is ON HOLD until Paper Publication

	Authors: Das, U., Wang, L.K., Smith, P., Shuman, S.		Authors: Das, U., Wang, L.K., Smith, P., Shuman, S.

	Description: Structure of bacterial polynucleotide kinase bound to GTP and RNA		Description: Structure of bacterial polynucleotide kinase bound to GTP and RNA

OCA: Protected "4qm6" [edit=sysop:move=sysop]

OCA — Wed, 25 Jun 2014 05:57:04 GMT

Protected "4qm6" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:57, 25 June 2014

OCA: New page: '''Unreleased structure''' The entry 4qm6 is ON HOLD Authors: Das, U., Wang, L.K., Smith, P., Shuman, S. Description: Structure of bacterial polynucleotide kinase bound to GTP and RNA

OCA — Wed, 25 Jun 2014 05:57:02 GMT

New page: '''Unreleased structure''' The entry 4qm6 is ON HOLD Authors: Das, U., Wang, L.K., Smith, P., Shuman, S. Description: Structure of bacterial polynucleotide kinase bound to GTP and RNA

New page

'''Unreleased structure'''

The entry 4qm6 is ON HOLD

Authors: Das, U., Wang, L.K., Smith, P., Shuman, S.

Description: Structure of bacterial polynucleotide kinase bound to GTP and RNA